Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 69 of 175
Found at i:20520296 original size:9 final size:9
Alignment explanation
Indices: 20520291--20520324 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20520281 TTTATAATTT
20520291 GAATAACTC
1 GAATAACTC
20520300 GAATAACTC
1 GAATAACTC
* *
20520309 GAATAATTT
1 GAATAACTC
20520318 GAATAAC
1 GAATAAC
20520325 AGATGAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (9 bp):
GAATAACTC
Found at i:20520424 original size:19 final size:19
Alignment explanation
Indices: 20520402--20520463 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
20520392 AAAATTACAA
20520402 AAAAAATCAAAATAATTTT
1 AAAAAATCAAAATAATTTT
20520421 AAAAAATTCAAAATAATTTT
1 AAAAAA-TCAAAATAATTTT
* *
20520441 TAAAATTCAAAAT-ATTTAT
1 AAAAAATCAAAATAATTT-T
20520460 AAAA
1 AAAA
20520464 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 17 0.45
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATCAAAATAATTTT
Found at i:20520426 original size:20 final size:20
Alignment explanation
Indices: 20520401--20520463 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
20520391 AAAAATTACA
*
20520401 AAAAAAATCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
20520421 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
20520441 -TAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
20520460 AAAA
1 AAAA
20520464 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 13 0.34
20 21 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:20520475 original size:18 final size:17
Alignment explanation
Indices: 20520418--20520475 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
20520408 TCAAAATAAT
*
20520418 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTC-AAA-AA
*
20520437 TTTTTAAAATTCAAAATA
1 TTTATAAAATTCAAAA-A
*
20520455 TTTATAAAAGTTCTAAAA
1 TTTATAAAA-TTCAAAAA
20520473 TTT
1 TTT
20520476 GCATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 16 0.48
19 16 0.48
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTATAAAATTCAAAAA
Found at i:20520882 original size:21 final size:21
Alignment explanation
Indices: 20520856--20520895 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20520846 ACCTTATCTA
*
20520856 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
20520877 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
20520896 CATTGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:20536371 original size:16 final size:16
Alignment explanation
Indices: 20536340--20536384 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
20536330 AAACATCATA
20536340 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
20536354 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
20536370 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
20536385 CCCAATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:20536382 original size:17 final size:16
Alignment explanation
Indices: 20536338--20536384 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
20536328 ATAAACATCA
20536338 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
20536353 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
20536369 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
20536385 CCCAATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:20538505 original size:27 final size:27
Alignment explanation
Indices: 20538475--20538532 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
20538465 TTCAGAGCTT
20538475 GCCATACGTACTATTCCTTCAAAGTTC
1 GCCATACGTACTATTCCTTCAAAGTTC
* *
20538502 GCCATACGTACTATTCCTTCAATGTTT
1 GCCATACGTACTATTCCTTCAAAGTTC
20538529 GCCA
1 GCCA
20538533 CACATATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.34
Consensus pattern (27 bp):
GCCATACGTACTATTCCTTCAAAGTTC
Found at i:20538544 original size:27 final size:27
Alignment explanation
Indices: 20538464--20538592 Score: 91
Period size: 27 Copynumber: 4.8 Consensus size: 27
20538454 AGAACATTTT
* * * *
20538464 CTTCAGAGCTTGCCATACGTACTATTC
1 CTTCAAAGTTTGCCACACATACTATTC
* * *
20538491 CTTCAAAGTTCGCCATACGTACTATTC
1 CTTCAAAGTTTGCCACACATACTATTC
*
20538518 CTTCAATGTTTGCCACACATA-TCATTC
1 CTTCAAAGTTTGCCACACATACT-ATTC
* * * * *
20538545 CTTCGAGGTTTGTCACACTTACAATT-
1 CTTCAAAGTTTGCCACACATACTATTC
* * *
20538571 CTTCAGAGTTAGCCATACATAC
1 CTTCAAAGTTTGCCACACATAC
20538593 ATTTCTTGCG
Statistics
Matches: 81, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
26 16 0.20
27 65 0.80
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (27 bp):
CTTCAAAGTTTGCCACACATACTATTC
Found at i:20538591 original size:53 final size:53
Alignment explanation
Indices: 20538462--20538775 Score: 171
Period size: 54 Copynumber: 6.1 Consensus size: 53
20538452 GCAGAACATT
* * * * * * *
20538462 TTCTTCAGAGCTT-GCCATACGTA-CTATTCCTTCAAAGTTCGCCATACGTACTA
1 TTCTTCAGAG-TTAGCCATACATATC-ATTCCTTCGAGGTTTGTCATACTTACAA
* * *
20538515 TTCCTTCA-ATGTTTGCCACACATATCATTCCTTCGAGGTTTGTCACACTTACAA
1 TT-CTTCAGA-GTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * **
20538569 TTCTTCAGAGTTAGCCATACATA-CATTTCTT-G-CG---G--A-AC--A-GT
1 TTCTTCAGAGTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * * * * * *
20538610 TTATTCAGAGCTT-GCCATACGTA-CTATTCCTTCAAAGTTTGCCATACGTACTA
1 TTCTTCAGAG-TTAGCCATACATATC-ATTCCTTCGAGGTTTGTCATACTTACAA
* * *
20538663 TTCCTTCA-ATGTTCGCCACACATATCATTCCTTCGAGGTTTATCATACTTACAA
1 TT-CTTCAGA-GTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
* * *
20538717 TTCTTCAGAGTTAGCCATACATATCATT-CTTCTAGGGTTGGTCATACTTACCA
1 TTCTTCAGAGTTAGCCATACATATCATTCCTTCGA-GGTTTGTCATACTTACAA
20538770 TTCTTC
1 TTCTTC
20538776 TCATTCAAGG
Statistics
Matches: 200, Mismatches: 37, Indels: 48
0.70 0.13 0.17
Matches are distributed among these distances:
41 19 0.09
42 9 0.05
44 3 0.01
45 1 0.00
47 2 0.01
49 1 0.00
50 3 0.01
51 1 0.00
52 13 0.06
53 70 0.35
54 76 0.38
55 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.37
Consensus pattern (53 bp):
TTCTTCAGAGTTAGCCATACATATCATTCCTTCGAGGTTTGTCATACTTACAA
Found at i:20538637 original size:23 final size:23
Alignment explanation
Indices: 20538611--20538665 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 23
20538601 CGGAACAGTT
*
20538611 TATTCAGAGCTTGCCATACGTAC
1 TATTCAAAGCTTGCCATACGTAC
*
20538634 TATTCCTTCAAAGTTTGCCATACGTAC
1 TA----TTCAAAGCTTGCCATACGTAC
20538661 TATTC
1 TATTC
20538666 CTTCAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
23 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (23 bp):
TATTCAAAGCTTGCCATACGTAC
Found at i:20538651 original size:27 final size:27
Alignment explanation
Indices: 20538621--20538680 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
20538611 TATTCAGAGC
20538621 TTGCCATACGTACTATTCCTTCAAAGT
1 TTGCCATACGTACTATTCCTTCAAAGT
*
20538648 TTGCCATACGTACTATTCCTTCAATGT
1 TTGCCATACGTACTATTCCTTCAAAGT
*
20538675 TCGCCA
1 TTGCCA
20538681 CACATATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.37
Consensus pattern (27 bp):
TTGCCATACGTACTATTCCTTCAAAGT
Found at i:20538692 original size:27 final size:27
Alignment explanation
Indices: 20538631--20538696 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
20538621 TTGCCATACG
* * *
20538631 TACTATTCCTTCAAAGTTTGCCATACG
1 TACTATTCCTTCAAAGTTCGCCACACA
*
20538658 TACTATTCCTTCAATGTTCGCCACACA
1 TACTATTCCTTCAAAGTTCGCCACACA
20538685 TA-TCATTCCTTC
1 TACT-ATTCCTTC
20538697 GAGGTTTATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.24, C:0.30, G:0.08, T:0.38
Consensus pattern (27 bp):
TACTATTCCTTCAAAGTTCGCCACACA
Found at i:20538747 original size:148 final size:148
Alignment explanation
Indices: 20538443--20538744 Score: 532
Period size: 148 Copynumber: 2.0 Consensus size: 148
20538433 ATACGCCACG
* *
20538443 ACATTTCTTGCAGAACATTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
1 ACATTTCTTGCAGAACAGTTTATTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
* *
20538508 CGTACTATTCCTTCAATGTTTGCCACACATATCATTCCTTCGAGGTTTGTCACACTTACAATTCT
66 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCGAGGTTTATCACACTTACAATTCT
20538573 TCAGAGTTAGCCATACAT
131 TCAGAGTTAGCCATACAT
* *
20538591 ACATTTCTTGCGGAACAGTTTATTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTTGCCATA
1 ACATTTCTTGCAGAACAGTTTATTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
*
20538656 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCGAGGTTTATCATACTTACAATTCT
66 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCGAGGTTTATCACACTTACAATTCT
20538721 TCAGAGTTAGCCATACAT
131 TCAGAGTTAGCCATACAT
20538739 ATCATT
1 A-CATT
20538745 CTTCTAGGGT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
148 142 0.97
149 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (148 bp):
ACATTTCTTGCAGAACAGTTTATTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCGAGGTTTATCACACTTACAATTCT
TCAGAGTTAGCCATACAT
Found at i:20538771 original size:27 final size:27
Alignment explanation
Indices: 20538705--20538776 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
20538695 TCGAGGTTTA
*
20538705 TCATACTTACAATTCTTC-AGAGTTAG
1 TCATACTTACCATTCTTCTAGAGTTAG
* * * * *
20538731 CCATACATATCATTCTTCTAGGGTTGG
1 TCATACTTACCATTCTTCTAGAGTTAG
20538758 TCATACTTACCATTCTTCT
1 TCATACTTACCATTCTTCT
20538777 CATTCAAGGT
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
26 14 0.39
27 22 0.61
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (27 bp):
TCATACTTACCATTCTTCTAGAGTTAG
Found at i:20539018 original size:27 final size:27
Alignment explanation
Indices: 20538843--20539050 Score: 176
Period size: 27 Copynumber: 7.7 Consensus size: 27
20538833 TGTAGAGTGC
* *
20538843 GCCACAAAGGCGTTCCT-TTCCATAGATC
1 GCCACAAAGGC-TT-CTATTTCATAGATT
20538871 GCCACAAAGGCTT-TAATTTCATAGATT
1 GCCACAAAGGCTTCT-ATTTCATAGATT
** *
20538898 TACACAAAGGCTT-TAATATCATAGATT
1 GCCACAAAGGCTTCT-ATTTCATAGATT
* * * * * *
20538925 TCTACAAAAGTTTCCATTTCAGAGATT
1 GCCACAAAGGCTTCTATTTCATAGATT
* *
20538952 GTCACAAAGTCTTAC-ATTTCATA-ATT
1 GCCACAAAGGCTT-CTATTTCATAGATT
*
20538978 GCCACAAAGGCTTCTACTTCATAGATT
1 GCCACAAAGGCTTCTATTTCATAGATT
20539005 GCCACAAAGGCTTCTATATT-ATAGATT
1 GCCACAAAGGCTTCTAT-TTCATAGATT
* *
20539032 GCCACAAAGACTTCCATTT
1 GCCACAAAGGCTTCTATTT
20539051 TCTAGCGCGT
Statistics
Matches: 148, Mismatches: 25, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
25 2 0.01
26 23 0.16
27 109 0.74
28 14 0.09
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (27 bp):
GCCACAAAGGCTTCTATTTCATAGATT
Found at i:20539786 original size:13 final size:13
Alignment explanation
Indices: 20539768--20539792 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20539758 TAAGTTATAT
20539768 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20539781 GTGTGAAAATTT
1 GTGTGAAAATTT
20539793 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20541549 original size:41 final size:41
Alignment explanation
Indices: 20541433--20541551 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
20541423 AATGGAAATT
* * * **
20541433 TTCAGGCTTAAAGTCTAGCAGGCTTAAGGCCGGTGATTTAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATAA
* * * *
20541474 TTCAGACTTTATGTCCAGCTGGCTTAACGTCGGTGAAATAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATAA
** *
20541515 TTTGGACTTTAAGTCTAGCAGGC-TAATTGCCGGTGAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAA-CGCCGGTGAA
20541552 TTGAATCAGG
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 3 0.05
41 58 0.95
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTAAGTCTAGCAGGCTTAACGCCGGTGAAATAA
Found at i:20547754 original size:13 final size:13
Alignment explanation
Indices: 20547736--20547760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20547726 TAAGTTATAT
20547736 GTGTGAAAATTTC
1 GTGTGAAAATTTC
20547749 GTGTGAAAATTT
1 GTGTGAAAATTT
20547761 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:20548215 original size:25 final size:25
Alignment explanation
Indices: 20548187--20548241 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
20548177 ATGCTTGAAT
* *
20548187 TTTTGTA-ATTGTTGATTATTTTGTG
1 TTTTGTACATTGATGA-TAATTTGTG
20548212 TTTT-TACATTGATGATAATTTGTG
1 TTTTGTACATTGATGATAATTTGTG
*
20548236 GTTTGT
1 TTTTGT
20548242 GATGTTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.18, C:0.02, G:0.20, T:0.60
Consensus pattern (25 bp):
TTTTGTACATTGATGATAATTTGTG
Found at i:20560050 original size:57 final size:57
Alignment explanation
Indices: 20560014--20560165 Score: 164
Period size: 59 Copynumber: 2.6 Consensus size: 57
20560004 GCCATAAGGG
*
20560014 CTTACCTTTCTAGGGTTTTGCCACAAAGGCTATCCTTTAACAGATTCAACTCAAAGA
1 CTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGATTCAACTCAAAGA
* * * ** *
20560071 CTTACCTTTCTAGAGTTTTGCCACAAAGGTTGTCCTCTTTAACAGGTTCGCCACAAA-A
1 CTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT-C-CTTTAACAGATTCAACTCAAAGA
* * * *
20560129 GTTTACCTTTCCAAAGTTTTTCCACAAAGGC-ATCCTT
1 -CTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTT
20560166 AAATAGAGAT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
56 3 0.04
57 31 0.39
58 3 0.04
59 42 0.53
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (57 bp):
CTTACCTTTCTAGAGTTTTGCCACAAAGGCTATCCTTTAACAGATTCAACTCAAAGA
Found at i:20560398 original size:53 final size:52
Alignment explanation
Indices: 20560314--20560464 Score: 189
Period size: 53 Copynumber: 2.9 Consensus size: 52
20560304 AATTTTTTCC
*
20560314 CATATGATACCATAACCCACCAGTTATAGTCTTACACGATATGGTCTTA-TTT
1 CATATGATACCATAACCCACCAGTTACAGTCTTACACGATATGGTC-TACTTT
* *
20560366 CGATATGATGCCATAACCCACCAATTACAGTCTTACACGATATGGTCTACTTTT
1 C-ATATGATACCATAACCCACCAGTTACAGTCTTACACGATATGGTCTAC-TTT
* * * * *
20560420 CATATGATCCCACAACCCATCAGTTACGGTCTTACA-GGTATGGTC
1 CATATGATACCATAACCCACCAGTTACAGTCTTACACGATATGGTC
20560465 CTTTAGCGCC
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
52 11 0.13
53 72 0.83
54 4 0.05
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (52 bp):
CATATGATACCATAACCCACCAGTTACAGTCTTACACGATATGGTCTACTTT
Found at i:20566607 original size:33 final size:33
Alignment explanation
Indices: 20566563--20566637 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
20566553 GATTACTCTC
* *
20566563 TTCACTTGTTTCTCATGCAAGCTCTCTTTCTTT
1 TTCACTCGTTTCTCATGCAAGCCCTCTTTCTTT
** *
20566596 TTCACTCGTTTCTTTTTCAAGCCCTCTTTCTTT
1 TTCACTCGTTTCTCATGCAAGCCCTCTTTCTTT
20566629 TTCACTCGT
1 TTCACTCGT
20566638 GTCTTTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.11, C:0.29, G:0.08, T:0.52
Consensus pattern (33 bp):
TTCACTCGTTTCTCATGCAAGCCCTCTTTCTTT
Found at i:20566609 original size:15 final size:15
Alignment explanation
Indices: 20566589--20566647 Score: 66
Period size: 15 Copynumber: 3.7 Consensus size: 15
20566579 GCAAGCTCTC
20566589 TTTCTTTTTCACTCG
1 TTTCTTTTTCACTCG
20566604 TTTCTTTTTCAAGCCCTC-
1 TTTCTTTTTC-A---CTCG
20566622 TTTCTTTTTCACTCG
1 TTTCTTTTTCACTCG
*
20566637 TGTCTTTTTCA
1 TTTCTTTTTCA
20566648 ACAACAACAC
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.08
15 20 0.53
16 1 0.03
17 1 0.03
18 10 0.26
19 3 0.08
ACGTcount: A:0.08, C:0.27, G:0.07, T:0.58
Consensus pattern (15 bp):
TTTCTTTTTCACTCG
Found at i:20566627 original size:18 final size:17
Alignment explanation
Indices: 20566580--20566632 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
20566570 GTTTCTCATG
20566580 CAAGCTCTCTTTCTTTTT
1 CAAGC-CTCTTTCTTTTT
20566598 C-A--CTCGTTTCTTTTT
1 CAAGCCTC-TTTCTTTTT
20566613 CAAGCCCTCTTTCTTTTT
1 CAAG-CCTCTTTCTTTTT
20566631 CA
1 CA
20566633 CTCGTGTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.10
15 10 0.33
16 1 0.03
17 1 0.03
18 12 0.40
19 3 0.10
ACGTcount: A:0.11, C:0.30, G:0.06, T:0.53
Consensus pattern (17 bp):
CAAGCCTCTTTCTTTTT
Found at i:20566643 original size:33 final size:33
Alignment explanation
Indices: 20566580--20566648 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
20566570 GTTTCTCATG
* *
20566580 CAAGCTCTCTTTCTTTTTCACTCGTTTCTTTTT
1 CAAGCCCTCTTTCTTTTTCACTCGTGTCTTTTT
20566613 CAAGCCCTCTTTCTTTTTCACTCGTGTCTTTTT
1 CAAGCCCTCTTTCTTTTTCACTCGTGTCTTTTT
20566646 CAA
1 CAA
20566649 CAACAACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.12, C:0.29, G:0.07, T:0.52
Consensus pattern (33 bp):
CAAGCCCTCTTTCTTTTTCACTCGTGTCTTTTT
Found at i:20567779 original size:16 final size:17
Alignment explanation
Indices: 20567745--20567786 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
20567735 TTTGCACACT
*
20567745 TTTTTTTATATTCGAAAC
1 TTTTTTT-TACTCGAAAC
20567763 TTTTTTTTACTCG-AAC
1 TTTTTTTTACTCGAAAC
20567779 TTTTTTTT
1 TTTTTTTT
20567787 GCTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTTTTTACTCGAAAC
Found at i:20567785 original size:17 final size:19
Alignment explanation
Indices: 20567742--20567786 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
20567732 TATTTTGCAC
*
20567742 ACTTTTTTTTATATTCGAA
1 ACTTTTTTTTATACTCGAA
20567761 AC-TTTTTTT-TACTCG-A
1 ACTTTTTTTTATACTCGAA
20567777 ACTTTTTTTT
1 ACTTTTTTTT
20567787 GCTTCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 7 0.29
19 2 0.08
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.62
Consensus pattern (19 bp):
ACTTTTTTTTATACTCGAA
Found at i:20571694 original size:22 final size:21
Alignment explanation
Indices: 20571666--20571735 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
20571656 AAAAAATTTT
20571666 AAAAAAGAACAAAATTTTGAAA
1 AAAAAAGAA-AAAATTTTGAAA
**
20571688 AAAAAAGAAAAAA-TAGGAAA
1 AAAAAAGAAAAAATTTTGAAA
*
20571708 AAAAGAATGAAAATA-TTTGAAA
1 AAAA-AA-GAAAAAATTTTGAAA
20571730 AAAAAA
1 AAAAAA
20571736 AGTGGCCTGC
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 9 0.22
21 8 0.20
22 24 0.59
ACGTcount: A:0.73, C:0.01, G:0.11, T:0.14
Consensus pattern (21 bp):
AAAAAAGAAAAAATTTTGAAA
Found at i:20573054 original size:6 final size:6
Alignment explanation
Indices: 20573037--20573088 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
20573027 TTTTATATTT
* * *
20573037 TTTTTG TCTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTA TTTTTA
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
20573085 TTTT
1 TTTT
20573089 ATTTTATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.04, C:0.02, G:0.12, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:20573082 original size:18 final size:18
Alignment explanation
Indices: 20573026--20573088 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
20573016 TAGTTTTATA
*
20573026 TTTTTATATTT-TTTTTG
1 TTTTTATTTTTGTTTTTG
* *
20573043 TCTTTGTTTTTGTTTTTG
1 TTTTTATTTTTGTTTTTG
* *
20573061 TTTTTGTTTTTGTTTTTA
1 TTTTTATTTTTGTTTTTG
20573079 TTTTTATTTT
1 TTTTTATTTT
20573089 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
17 8 0.21
18 31 0.79
ACGTcount: A:0.06, C:0.02, G:0.10, T:0.83
Consensus pattern (18 bp):
TTTTTATTTTTGTTTTTG
Found at i:20579847 original size:26 final size:26
Alignment explanation
Indices: 20579694--20579848 Score: 145
Period size: 26 Copynumber: 6.0 Consensus size: 26
20579684 TCAAATAGGT
* * *
20579694 TACACCACAAAGGC-AACATACTGAA
1 TACACCATAAAGGCTATCATACAGAA
* * * *
20579719 TACACTACAAAGGCTACCATACAAAA
1 TACACCATAAAGGCTATCATACAGAA
*
20579745 TA-AGCCATAAAGGCTATCATACAAAA
1 TACA-CCATAAAGGCTATCATACAGAA
* *
20579771 TACACCATAAAGTCTATCATGCA-AA
1 TACACCATAAAGGCTATCATACAGAA
** * *
20579796 TATGCCAAAAAGGTTATCATACAGAA
1 TACACCATAAAGGCTATCATACAGAA
*
20579822 TACACCATAAAGGCTATCATATAGAA
1 TACACCATAAAGGCTATCATACAGAA
20579848 T
1 T
20579849 GCCACAAAAG
Statistics
Matches: 106, Mismatches: 20, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
25 33 0.31
26 72 0.68
27 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.11, T:0.20
Consensus pattern (26 bp):
TACACCATAAAGGCTATCATACAGAA
Found at i:20579858 original size:51 final size:51
Alignment explanation
Indices: 20579717--20579842 Score: 162
Period size: 51 Copynumber: 2.5 Consensus size: 51
20579707 CAACATACTG
* * * * *
20579717 AATACACTACAAAGGCTACCATACAAAATAAGCCATAAAGGCTATCATACAA
1 AATACACCATAAAGGCTATCATAC-AAATATGCCAAAAAGGCTATCATACAA
* * * *
20579769 AATACACCATAAAGTCTATCATGCAAATATGCCAAAAAGGTTATCATACAG
1 AATACACCATAAAGGCTATCATACAAATATGCCAAAAAGGCTATCATACAA
20579820 AATACACCATAAAGGCTATCATA
1 AATACACCATAAAGGCTATCATA
20579843 TAGAATGCCA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 44 0.70
52 19 0.30
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (51 bp):
AATACACCATAAAGGCTATCATACAAATATGCCAAAAAGGCTATCATACAA
Found at i:20585265 original size:41 final size:41
Alignment explanation
Indices: 20585172--20585286 Score: 113
Period size: 41 Copynumber: 2.8 Consensus size: 41
20585162 ATTCTACCTT
**
20585172 TCGGGGCTTTAGCATCGTTTTTAAAAAAAGCGCCGCTAAAGC
1 TCGGGGCTTTAGCGGCG-TTTTAAAAAAAGCGCCGCTAAAGC
* ** ** * *
20585214 TCAGATCTTTAGCGGCGTTTTCCAATAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTAAAAAAAGCGCCGCTAAAGC
* **
20585255 TCGGGGCTTTAGTGGCGTTTTTGAAAAAGCGC
1 TCGGGGCTTTAGCGGCGTTTTAAAAAAAGCGC
20585287 AGCAAAAACA
Statistics
Matches: 57, Mismatches: 16, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
41 45 0.79
42 12 0.21
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTAAAAAAAGCGCCGCTAAAGC
Found at i:20585717 original size:14 final size:15
Alignment explanation
Indices: 20585689--20585721 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
20585679 AAGGTTTATA
20585689 GATTATGGAATTAGG
1 GATTATGGAATTAGG
20585704 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
20585718 GATT
1 GATT
20585722 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:20585948 original size:95 final size:95
Alignment explanation
Indices: 20585806--20585996 Score: 294
Period size: 95 Copynumber: 2.0 Consensus size: 95
20585796 GTTTATGGAT
* * *
20585806 TCGGTGTTAGGTTAAGGTTTAGGGTTTAGATTAATTAGTGTATTTTAATTTATATATTAAATAAT
1 TCGGTGTTAGGTTAAGGTTTAGGATTTAAATTAATTAGTGTATTTTAATTTATATATTAAATAAG
20585871 GTTTAGGGGTTAGGGGTTAGGGATTTGGGG
66 GTTTAGGGGTTAGGGGTTAGGGATTTGGGG
* *
20585901 TCGG-GTTAGGGTTAGGGTTTAGGATTTAAATTAATTAGTGTTTTTTAATTTATATATTAAATAA
1 TCGGTGTTA-GGTTAAGGTTTAGGATTTAAATTAATTAGTGTATTTTAATTTATATATTAAATAA
* * *
20585965 GGTTTAGGGGTTAGTGGTTTGGGGTTTGGGG
65 GGTTTAGGGGTTAGGGGTTAGGGATTTGGGG
20585996 T
1 T
20585997 TTGGGAGTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 4 0.05
95 83 0.95
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.44
Consensus pattern (95 bp):
TCGGTGTTAGGTTAAGGTTTAGGATTTAAATTAATTAGTGTATTTTAATTTATATATTAAATAAG
GTTTAGGGGTTAGGGGTTAGGGATTTGGGG
Found at i:20585990 original size:14 final size:14
Alignment explanation
Indices: 20585965--20586019 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
20585955 TATTAAATAA
20585965 GGTTTAGGGGTTAGT
1 GGTTT-GGGGTTAGT
* *
20585980 GGTTTGGGGTTTGG
1 GGTTTGGGGTTAGT
20585994 GGTTTGGGAGTTAGT
1 GGTTTGGG-GTTAGT
* *
20586009 GATTTAGGGTT
1 GGTTTGGGGTT
20586020 TAGAGATTCG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 18 0.55
15 15 0.45
ACGTcount: A:0.11, C:0.00, G:0.47, T:0.42
Consensus pattern (14 bp):
GGTTTGGGGTTAGT
Found at i:20586007 original size:29 final size:29
Alignment explanation
Indices: 20585965--20586020 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
20585955 TATTAAATAA
* *
20585965 GGTTTAGGGGTTAGTGGTTTGGGGTTTGG
1 GGTTTAGGGGTTAGTGATTTAGGGTTTGG
20585994 GGTTT-GGGAGTTAGTGATTTAGGGTTT
1 GGTTTAGGG-GTTAGTGATTTAGGGTTT
20586021 AGAGATTCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.11, C:0.00, G:0.46, T:0.43
Consensus pattern (29 bp):
GGTTTAGGGGTTAGTGATTTAGGGTTTGG
Found at i:20587073 original size:124 final size:125
Alignment explanation
Indices: 20586892--20587123 Score: 405
Period size: 124 Copynumber: 1.9 Consensus size: 125
20586882 ATAATTTTTT
20586892 GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCCATTTTAGC
1 GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCCATTTTAGC
* * *
20586957 ATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTTGCGGCATTTTGCAATA
66 ATAACAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTGCAATA
*
20587017 GCGGCGTTTTTAT-AAAATACGCCAC-AAAAATAATTTTATTTTAAAAAAATAGCGCCATTTTAG
1 GCGGCGTTTTTATGAAAA-ACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCCATTTTAG
20587080 CATAACAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTT
65 CATAACAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTT
20587124 ACGGCGTTTT
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
124 82 0.80
125 20 0.20
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (125 bp):
GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCGCCATTTTAGC
ATAACAAAACAGTATCGTTTTATTCCAAATAAAATAATTTTTTTGCGGCATTTTGCAATA
Found at i:20591903 original size:43 final size:43
Alignment explanation
Indices: 20591851--20592207 Score: 462
Period size: 43 Copynumber: 8.3 Consensus size: 43
20591841 AGATTATGTT
** *
20591851 TTTAGCGGCGTTTGTAAGAAAAGCGCCGCTAAAGGTCATAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
20591894 TATGGCGGCGTTTGAGGGAACAGCGCCACTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
** * * *
20591937 AATAGCGGCGTTTGTTGGAAAAGCGCCACTAATGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
20591980 TATAGCGACGTTTTTGGGAAAAGCGCCGCTAATGGTCATGGTA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* **
20592023 TTTAGCGGCGTTTTTGAAAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* *
20592066 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGTA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
20592109 TTTAGCGGCGTTTATGGGAAAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
20592152 TTTAGCGGCGTTTTTGAGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
*
20592195 TTTAGCGGTGTTT
1 TTTAGCGGCGTTT
20592208 ATTTCTAAAA
Statistics
Matches: 276, Mismatches: 38, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 276 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:20593433 original size:18 final size:19
Alignment explanation
Indices: 20593388--20593436 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20593378 TCAACTTTTG
*
20593388 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
20593407 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
*
20593426 TAAA-ATTTATA
1 AAAATATTTATA
20593437 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:20593825 original size:21 final size:21
Alignment explanation
Indices: 20593801--20593840 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
20593791 ACCTTTTCTA
*
20593801 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
20593822 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
20593841 CGTTATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:20594350 original size:18 final size:19
Alignment explanation
Indices: 20594305--20594350 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
20594295 TCGAACATAA
*
20594305 AATATATAAATTACAAAAT
1 AATATATAAAGTACAAAAT
*
20594324 AGA-AAATAAAGT-CAAAAT
1 A-ATATATAAAGTACAAAAT
20594342 AATATATAA
1 AATATATAA
20594351 CTTACATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.05
18 12 0.55
19 8 0.36
20 1 0.05
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
AATATATAAAGTACAAAAT
Found at i:20594501 original size:2 final size:2
Alignment explanation
Indices: 20594494--20594522 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20594484 CATTACAAAA
20594494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20594523 ACCAATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20594587 original size:17 final size:18
Alignment explanation
Indices: 20594567--20594600 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20594557 GCATAAAAGT
20594567 AAAATAAAAAT-AACAAC
1 AAAATAAAAATGAACAAC
*
20594584 AAAATGAAAATGAACAA
1 AAAATAAAAATGAACAA
20594601 TTAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.09, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAATAAAAATGAACAAC
Found at i:20596000 original size:72 final size:72
Alignment explanation
Indices: 20595883--20596025 Score: 286
Period size: 72 Copynumber: 2.0 Consensus size: 72
20595873 TAGACTTTTG
20595883 CCTTCCTCTTATAATTAAAAAAGAAGCAAAAACGAAATCACCGTTTACCATTTTAAATGGTGATT
1 CCTTCCTCTTATAATTAAAAAAGAAGCAAAAACGAAATCACCGTTTACCATTTTAAATGGTGATT
20595948 TAGCACA
66 TAGCACA
20595955 CCTTCCTCTTATAATTAAAAAAGAAGCAAAAACGAAATCACCGTTTACCATTTTAAATGGTGATT
1 CCTTCCTCTTATAATTAAAAAAGAAGCAAAAACGAAATCACCGTTTACCATTTTAAATGGTGATT
20596020 TAGCAC
66 TAGCAC
20596026 TAGCTGCATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (72 bp):
CCTTCCTCTTATAATTAAAAAAGAAGCAAAAACGAAATCACCGTTTACCATTTTAAATGGTGATT
TAGCACA
Found at i:20597032 original size:178 final size:177
Alignment explanation
Indices: 20596118--20597872 Score: 2326
Period size: 178 Copynumber: 9.9 Consensus size: 177
20596108 TAAAGGGTGA
* *
20596118 TTCATGCTATTTTAATAAATAATTTTGAAGTTATATTA-TTTAAATGGTGATTTAGCACTAGCCT
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * * *
20596182 CATTGTTGTTAGAGTTTTACCCTCTTCTTATAATTAAAAAAAGAAAGAAGCAAAAACAAAATCAC
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAA-TCAAAAAA-AAA-AAGCAAAAACGAAATCAC
* * *
20596247 CGTTTACCATTTTAAATGGTGATTTTGCATATCCCATTAGTACTATTCAT
128 CGTTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* *
20596297 TTCATACTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCATTAGCCG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * *
20596362 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATTAAAAAGAAAAAGAAAAAATGAAATCATCGT
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATCAAAAAAAAAAAGCAAAAACGAAATCACCGT
* * *
20596427 TTACCATTTTAAAGGGTGATTTAGCAGATCTCATTAGTACTATTCAT
131 TTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* * * *
20596474 TTCATGTTATTTTAATAAATAATTTTGAAGTTATATTATTTTAAAT-GTGATTTAGCACTAGACA
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * * * *
20596538 CATTGCTGTTAGAATTTTTCCATCCTCTTAT-A--AATAAAAAAAA-CAAAAGCAAAATCATCGT
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATCAAAAAAAAAAAGCAAAAACGAAATCACCGT
*
20596599 TTACCATTTTAAATGGTGATTTAGCAGATCTCATTAGTACTGTTCAT
131 TTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* * *
20596646 TTCATGCTACTTTAATAAATAATTTTGAAGTTATATTATTTTAAATGGTGATTTAGCACTAGGCG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * **
20596711 CATTGCTATTAGAGTTTTGCCTTCCTCTTATAATTAAAAACAAAAA-CAAAAACAAAATCATTGT
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATCAAAAAAAAAAAGCAAAAACGAAATCACCGT
* * * * *
20596775 TTAACATTTTAAAGGGTGATTTAGTAGACCCCATTAGTACTGTTCAG
131 TTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
20596822 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* *
20596887 CATTGCTG-TAGGAGTTTTTCCTTCCTCTTATAATGCAAAAAAAAAAAGCAAAAATGAAATCACC
66 CATTGCTGTTA-GAGTTTTGCCTTCCTCTTATAAT-CAAAAAAAAAAAGCAAAAACGAAATCACC
* * *
20596951 GTTTACCATTTTAAAGGGTGATTTAGTAGATCCCATTAGTACCGTTCAT
129 GTTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
** *
20597000 TTCACACTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCA
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
*
20597065 CATTGCTGTAAGAGTTTTGCCTTCCTCTTATAATTC-AAAAAAAAAAGCAAAAACGAAATCACCG
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAA-TCAAAAAAAAAAAGCAAAAACGAAATCACCG
* *
20597129 TTTACCATTTTAAAAGGTGATTTAGTAGATCCCATTAGTACTGTTCAT
130 TTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* * * *
20597177 TTCATGGTATTTTAATAAATAATTTTGAATTTATATTTATTTTAAATGGTGATTTAGCACTAGAC
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATA-CTATTTTAAATGGTGATTTAGCACTAGCC
** * * * *
20597242 AAATTGTTGTTAAAGTTTTGCCCTCCTCTTATAATTC-AAAAAAAAAAGCAAAAAGTGAAATCAC
65 GCATTGCTGTTAGAGTTTTGCCTTCCTCTTATAA-TCAAAAAAAAAAAGCAAAAA-CGAAATCAC
* * * *
20597306 CATTTACCATTTTAAATGATGATTTATCAGATCCCATTAGTATTGTTCAT
128 CGTTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* * *
20597356 TTCATGCTACTTTAATAAATAATTTTGAAGTTATACTATTTTTAATGGTGATTTAGCACTAGTCG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * *
20597421 TATTGTTGTTAGAGTTTTGCCTTCCTCTTATAATTAAAAAGAAAAAAGAAAAAACGAAATCACCA
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATCAAAAA-AAAAAAGCAAAAACGAAATCACCG
*
20597486 TTTACCATTTTAAATGGTGATTTAGCAGAACCCATTAGTA-TGGTTCAT
130 TTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACT-GTTCAT
** * *
20597534 CCCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAACTG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* *
20597599 CATTACTGTTAGAGTTTTGCATTCCTCTTATAATTCAAACAAACAAAAAAAAAAGCAAAAACGAA
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAA-T----C--A-AAAAAAAAAAGCAAAAACGAA
* * * *
20597664 ATCACCTTTTACCATTTTAAATGGTGATTTAGCATATCCCATTGGTACAGTTCAT
123 ATCACCGTTTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
* * *
20597719 TTCATGCTATTTTAATAAATAATTTTGAAGTTATATTATTTCAAATGGTGATTTAGCACTAGTCG
1 TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
* * * * * *
20597784 CATTGCTATAAAAGTTTTGCCCTCCTCTTATAATTCATAAAAAGAAGAAGCAGAAACGAAATCAC
66 CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAA-TCA-AAAAA-AAAAAGCAAAAACGAAATCAC
*
20597849 TGTTTACCATTTTAAATGGTGATT
128 CGTTTACCATTTTAAATGGTGATT
20597873 AGACACATTA
Statistics
Matches: 1405, Mismatches: 146, Indels: 49
0.88 0.09 0.03
Matches are distributed among these distances:
172 103 0.07
173 52 0.04
174 1 0.00
175 3 0.00
176 200 0.14
177 219 0.16
178 428 0.30
179 147 0.10
180 94 0.07
181 1 0.00
185 153 0.11
186 4 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (177 bp):
TTCATGCTATTTTAATAAATAATTTTGAAGTTATACTATTTTAAATGGTGATTTAGCACTAGCCG
CATTGCTGTTAGAGTTTTGCCTTCCTCTTATAATCAAAAAAAAAAAGCAAAAACGAAATCACCGT
TTACCATTTTAAATGGTGATTTAGCAGATCCCATTAGTACTGTTCAT
Found at i:20598048 original size:24 final size:25
Alignment explanation
Indices: 20597996--20598059 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 25
20597986 CATTTCATGG
20597996 TATTTTAATAAATAATTTTGAAGTTATAT
1 TATTTTAAT-AATAATTTT--A-TTATAT
20598025 TATTTTAATAATAATTTT-TTATAT
1 TATTTTAATAATAATTTTATTATAT
*
20598049 TATTTAAATAA
1 TATTTTAATAA
20598060 AAAATAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 16 0.47
28 9 0.26
29 9 0.26
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
TATTTTAATAATAATTTTATTATAT
Found at i:20603947 original size:30 final size:29
Alignment explanation
Indices: 20603913--20603994 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 29
20603903 AGCAATGTGG
20603913 GGGCCTTAGCACAATACAGTAACAGAGTGT
1 GGGCCTTAGC-CAATACAGTAACAGAGTGT
20603943 GGGCCTTAGCCCAATACAGTAACAGAGTGT
1 GGGCCTTAG-CCAATACAGTAACAGAGTGT
20603973 GGGCCTTAGTCCAATACAGTAA
1 GGGCCTTAG-CCAATACAGTAA
20603995 TAGTGCAAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 49 0.98
31 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (29 bp):
GGGCCTTAGCCAATACAGTAACAGAGTGT
Found at i:20603977 original size:60 final size:60
Alignment explanation
Indices: 20603882--20603994 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
20603872 AGAATCAGTC
* * *
20603882 TGGGCCTGAGCCCTATATAGTAGCAATGTGGGGGCCTTAG-CACAATACAGTAACAGAGTG
1 TGGGCCTGAGCCCAATACAGTAACAATGTGGGGGCCTTAGTC-CAATACAGTAACAGAGTG
* *
20603942 TGGGCCTTAGCCCAATACAGTAACAGA-GTGTGGGCCTTAGTCCAATACAGTAA
1 TGGGCCTGAGCCCAATACAGTAACA-ATGTGGGGGCCTTAGTCCAATACAGTAA
20603995 TAGTGCAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (60 bp):
TGGGCCTGAGCCCAATACAGTAACAATGTGGGGGCCTTAGTCCAATACAGTAACAGAGTG
Found at i:20604140 original size:26 final size:26
Alignment explanation
Indices: 20604106--20604207 Score: 107
Period size: 26 Copynumber: 3.9 Consensus size: 26
20604096 CACTAATATT
20604106 GCAGCAAAGCTGCCAGTAATAGTAAC
1 GCAGCAAAGCTGCCAGTAATAGTAAC
* * * * *
20604132 GCAGTAAAGCTGCCAATAACATTAAT
1 GCAGCAAAGCTGCCAGTAATAGTAAC
* *
20604158 GCAACAGAGCTGCCAGT-ATCAGTAAC
1 GCAGCAAAGCTGCCAGTAAT-AGTAAC
* *
20604184 ACAGCAAAGCTGCTAGTAATAGTA
1 GCAGCAAAGCTGCCAGTAATAGTA
20604208 CTTGTGGTAA
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
25 1 0.02
26 55 0.95
27 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.19
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTAAC
Found at i:20604473 original size:54 final size:53
Alignment explanation
Indices: 20604403--20604761 Score: 304
Period size: 54 Copynumber: 6.7 Consensus size: 53
20604393 TATAACGGTC
20604403 ATTTTACCCTAT-AGGGGTATTTCGATAGTTTTACCCATCGAGGATATTTCGATA
1 ATTTTACCC-ATCAGGGGTATTTCGATA-TTTTACCCATCGAGGATATTTCGATA
* * *
20604457 ATTTTACCCATCAGGGGTATTTTGGTAGTTTTACCCATCGAGGATATTAT-GGTA
1 ATTTTACCCATCAGGGGTATTTCGATA-TTTTACCCATCGAGGATATT-TCGATA
* * ** *
20604511 ATTTTACCCATCAAGAGTATTTC-AGTCATTTTACTTATCGAGGATATTTC-AGTC
1 ATTTTACCCATCAGGGGTATTTCGA-T-ATTTTACCCATCGAGGATATTTCGA-TA
* *
20604565 ATTTTACCCATC-GAGGGTATTTC-AGTAATTTTACCCATTGATGG-TATTTCGGTA
1 ATTTTACCCATCAG-GGGTATTTCGA-T-ATTTTACCCATCGA-GGATATTTCGATA
* * ** *
20604619 ATTTTATCCATCAGGGGTATTTCGATAATTTTACCTATCGAGGGCATTTCAATA
1 ATTTTACCCATCAGGGGTATTTCGAT-ATTTTACCCATCGAGGATATTTCGATA
* * * * *
20604673 ATTTTACCCATC-GAGGGTAATGCAATCATTTTACCCAT-GAGGGTATTTCGGTA
1 ATTTTACCCATCAG-GGGTATTTCGAT-ATTTTACCCATCGAGGATATTTCGATA
* * * *
20604726 ATTTTACCCTTCGGGGGTAATTCAATCATTTTACCC
1 ATTTTACCCATCAGGGGTATTTCGAT-ATTTTACCC
20604762 TTCGGGAGTA
Statistics
Matches: 255, Mismatches: 36, Indels: 29
0.80 0.11 0.09
Matches are distributed among these distances:
53 50 0.20
54 199 0.78
55 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.39
Consensus pattern (53 bp):
ATTTTACCCATCAGGGGTATTTCGATATTTTACCCATCGAGGATATTTCGATA
Found at i:20604518 original size:81 final size:81
Alignment explanation
Indices: 20604388--20604761 Score: 323
Period size: 81 Copynumber: 4.6 Consensus size: 81
20604378 TTTATCTCCT
** * * *
20604388 AGGGGTATAACGGTCATTTTACCCTATAG-GGGTATTTC-GATAGTTTTACCCATCGAGGATATT
1 AGGGGTATTTCGGTAATTTTACCC-ATCGAGGGTATTTCAG-TAATTTTACCCATCGAGGATATT
20604451 TCGATAATTTTACCCATC
64 TCGATAATTTTACCCATC
* * * * *
20604469 AGGGGTATTTTGGTAGTTTTACCCATCGAGGATATTAT-GGTAATTTTACCCATC-AAGAGTATT
1 AGGGGTATTTCGGTAATTTTACCCATCGAGGGTATT-TCAGTAATTTTACCCATCGAGGA-TATT
* **
20604532 TC-AGTCATTTTACTTATC
64 TCGA-TAATTTTACCCATC
* * * *
20604550 -GAGGATATTTCAGTCATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATTGATGG-TATT
1 AG-GGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATCGA-GGATATT
* *
20604613 TCGGTAATTTTATCCATC
64 TCGATAATTTTACCCATC
* * * * * * *
20604631 AGGGGTATTTCGATAATTTTACCTATCGAGGGCATTTCAATAATTTTACCCATCGAGGGTAATGC
1 AGGGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATCGAGGATATTTC
* * *
20604696 AATCATTTTACCCATG
66 GATAATTTTACCCATC
* * * * *
20604712 A-GGGTATTTCGGTAATTTTACCCTTCGGGGGTAATTCAATCATTTTACCC
1 AGGGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCC
20604762 TTCGGGAGTA
Statistics
Matches: 233, Mismatches: 48, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
80 53 0.23
81 175 0.75
82 4 0.02
83 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.38
Consensus pattern (81 bp):
AGGGGTATTTCGGTAATTTTACCCATCGAGGGTATTTCAGTAATTTTACCCATCGAGGATATTTC
GATAATTTTACCCATC
Found at i:20604756 original size:27 final size:27
Alignment explanation
Indices: 20604403--20604775 Score: 220
Period size: 27 Copynumber: 13.9 Consensus size: 27
20604393 TATAACGGTC
* * *
20604403 ATTTTACCCTATAG-GGGTATTTCGATA
1 ATTTTACCC-ATCGAGGGTAATTCAATA
* * * *
20604430 GTTTTACCCATCGAGGATATTTCGATA
1 ATTTTACCCATCGAGGGTAATTCAATA
* ***
20604457 ATTTTACCCATC-AGGGGTATTTTGGTA
1 ATTTTACCCATCGA-GGGTAATTCAATA
* * *
20604484 GTTTTACCCATCGAGGAT-ATT-ATGGTA
1 ATTTTACCCATCGAGGGTAATTCA--ATA
* * * * *
20604511 ATTTTACCCATCAAGAGTATTTCAGTC
1 ATTTTACCCATCGAGGGTAATTCAATA
** * * * *
20604538 ATTTTACTTATCGAGGATATTTCAGTC
1 ATTTTACCCATCGAGGGTAATTCAATA
* *
20604565 ATTTTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCATCGAGGGTAATTCAATA
* * * **
20604592 ATTTTACCCATTGATGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTAATTCAATA
* * *
20604619 ATTTTATCCATC-AGGGGTATTTCGATA
1 ATTTTACCCATCGA-GGGTAATTCAATA
* * *
20604646 ATTTTACCTATCGAGGGCATTTCAATA
1 ATTTTACCCATCGAGGGTAATTCAATA
* *
20604673 ATTTTACCCATCGAGGGTAATGCAATC
1 ATTTTACCCATCGAGGGTAATTCAATA
* **
20604700 ATTTTACCCAT-GAGGGTATTTCGGTA
1 ATTTTACCCATCGAGGGTAATTCAATA
* * *
20604726 ATTTTACCCTTCGGGGGTAATTCAATC
1 ATTTTACCCATCGAGGGTAATTCAATA
*
20604753 ATTTTACCCTTCG-GGAGTAATTC
1 ATTTTACCCATCGAGG-GTAATTC
20604776 GGTCATTTGT
Statistics
Matches: 282, Mismatches: 53, Indels: 22
0.79 0.15 0.06
Matches are distributed among these distances:
26 29 0.10
27 248 0.88
28 4 0.01
29 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTAATTCAATA
Found at i:20610942 original size:10 final size:10
Alignment explanation
Indices: 20610927--20610969 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
20610917 ATTAACATGT
20610927 TTAATTTTAA
1 TTAATTTTAA
20610937 TTAATTTTATAA
1 TTAA-TTT-TAA
* *
20610949 TAAATTTTTA
1 TTAATTTTAA
20610959 TTAATTTTAA
1 TTAATTTTAA
20610969 T
1 T
20610970 CGTTTTCAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 15 0.56
11 6 0.22
12 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:20614597 original size:16 final size:17
Alignment explanation
Indices: 20614560--20614602 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
20614550 AAATTTAAAC
20614560 ATTTT-ATTAAAATAAT
1 ATTTTAATTAAAATAAT
*
20614576 AGTTTAATTAAAATAAT
1 ATTTTAATTAAAATAAT
*
20614593 -TTTTATTTAA
1 ATTTTAATTAA
20614603 TAAATTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTTAATTAAAATAAT
Found at i:20620603 original size:3 final size:3
Alignment explanation
Indices: 20620595--20620628 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
20620585 GTACTCAATA
*
20620595 TAT TAT TAT TAT TAT GAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20620629 CCTTTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20628128 original size:45 final size:44
Alignment explanation
Indices: 20628030--20628468 Score: 343
Period size: 44 Copynumber: 10.0 Consensus size: 44
20628020 GGACCTACTA
* * *** * *
20628030 TCTTTGATCTACTTCA-CGCTAGTACATGAAGATAAGATCTATT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
* * *
20628073 GTCTTCGATCTACTTCACCACCAATATGGGGAGACAAGATCTGTT
1 -TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
* *** *
20628118 ATCTTTGATCTACTTCA-CGCCAGTACCTGAAGACAAGATCTAATT
1 -TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCT-GTT
* * *
20628163 T-TTTCGATCTACTCCACCACTAGTATGGGGAGACAAGATCTGTT
1 TCTTT-GATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
* *** * *
20628207 TCTTTGATCTACTTCA-CGCCAGTACATGAAAATAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TT
* * * * *
20628251 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTGGT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
* ***
20628295 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TT
* * * ** *
20628339 TCTTCGATCTGCTTCGCCACCAGTATGGGAAGGTAAGATCTGGT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
* ***
20628383 TCTTTGATCTACTTCA-CGCCAGTACATGAAGACAAGATCTGCTT
1 TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTG-TT
* * *
20628427 T-TTTCGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCTG
1 TCTTT-GATCTACTTCACCACCAGTATGGGAAGACAAGATCTG
20628469 GTATATTCGA
Statistics
Matches: 300, Mismatches: 83, Indels: 23
0.74 0.20 0.06
Matches are distributed among these distances:
43 62 0.21
44 125 0.42
45 113 0.38
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTT
Found at i:20628258 original size:88 final size:88
Alignment explanation
Indices: 20628030--20628470 Score: 641
Period size: 88 Copynumber: 5.0 Consensus size: 88
20628020 GGACCTACTA
* * * * *
20628030 TCTTTGATCTACTTCACGCTAGTACATGAAGATAAGATCT-ATTGTCTTCGATCTACTTCACCAC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTT-TCTTCGATCTGCTTCGCCAC
* * * *
20628094 CAATATGGGGAGACAAGATCTGTT
65 CAGTATGGGAAGGCAAGATCTGGT
* ** * * * *
20628118 ATCTTTGATCTACTTCACGCCAGTACCTGAAGACAAGATCTAATTTTTTCGATCTACTCCACCAC
1 -TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCAC
* * * *
20628183 TAGTATGGGGAGACAAGATCTGTT
65 CAGTATGGGAAGGCAAGATCTGGT
* *
20628207 TCTTTGATCTACTTCACGCCAGTACATGAAAATAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
20628272 AGTATGGGAAGGCAAGATCTGGT
66 AGTATGGGAAGGCAAGATCTGGT
20628295 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
*
20628360 AGTATGGGAAGGTAAGATCTGGT
66 AGTATGGGAAGGCAAGATCTGGT
*
20628383 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTTTTCGATCTGCTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
20628448 AGTATGGGAAGGCAAGATCTGGT
66 AGTATGGGAAGGCAAGATCTGGT
20628471 ATATTCGATC
Statistics
Matches: 326, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
88 246 0.75
89 77 0.24
90 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (88 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACC
AGTATGGGAAGGCAAGATCTGGT
Found at i:20644729 original size:7 final size:7
Alignment explanation
Indices: 20644717--20644752 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
20644707 TGGAAATTGT
20644717 GGAAAGG
1 GGAAAGG
20644724 GGAAAGG
1 GGAAAGG
20644731 GGAAAGG
1 GGAAAGG
20644738 GGAAAGG
1 GGAAAGG
20644745 GGAAAGG
1 GGAAAGG
20644752 G
1 G
20644753 CTTGGAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (7 bp):
GGAAAGG
Found at i:20644985 original size:14 final size:15
Alignment explanation
Indices: 20644960--20644988 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20644950 ATCACTAGAT
20644960 AAATCAAAATTTAAA
1 AAATCAAAATTTAAA
20644975 AAATC-AAATTTAAA
1 AAATCAAAATTTAAA
20644989 CTAATTATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATCAAAATTTAAA
Found at i:20645063 original size:29 final size:29
Alignment explanation
Indices: 20645030--20645086 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
20645020 AATTTGATCT
* *
20645030 TTATCCAACCAATTTTAAATATTCAATCA
1 TTATCCAACCAACTTCAAATATTCAATCA
*
20645059 TTATCCAACCAACTTCAAATCTTCAATC
1 TTATCCAACCAACTTCAAATATTCAATC
20645087 TTTCAACCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (29 bp):
TTATCCAACCAACTTCAAATATTCAATCA
Found at i:20645437 original size:18 final size:19
Alignment explanation
Indices: 20645404--20645440 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20645394 TGATAGATGA
*
20645404 TAGATGATGTTTTATTTTT
1 TAGATAATGTTTTATTTTT
20645423 TAGATAATG-TTTATTTTT
1 TAGATAATGTTTTATTTTT
20645441 ATTGACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (19 bp):
TAGATAATGTTTTATTTTT
Found at i:20654140 original size:13 final size:13
Alignment explanation
Indices: 20654124--20654158 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
20654114 TAAAACCCAA
*
20654124 ATATAAAATATAT
1 ATATAAAATAAAT
20654137 ATATAAAATAAAT
1 ATATAAAATAAAT
20654150 ATAATAAAA
1 AT-ATAAAA
20654159 GTCCAATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATATAAAATAAAT
Found at i:20656824 original size:14 final size:14
Alignment explanation
Indices: 20656807--20656834 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20656797 CTCACATTTC
20656807 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
20656821 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
20656835 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:20656825 original size:19 final size:18
Alignment explanation
Indices: 20656787--20656831 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
20656777 TACGGTACGC
20656787 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
20656804 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
20656823 TTCTTTTCT
1 TTCTTTTCT
20656832 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:20659853 original size:58 final size:56
Alignment explanation
Indices: 20659791--20659900 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 56
20659781 TATATTTTTA
20659791 TATT-ATTATATATCATGATTTTAGTAAATTCATA-TAAGAATAATTATATTAAGAATTT
1 TATTAATTATATAT-AT--TTTTAGTAAATT-ATATTAAGAATAATTATATTAAGAATTT
* * *
20659849 TATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
1 TATT-AATTATATATATTTTTAGTAAATTATA-TTAAGAATAATTATATTAA
20659901 AATATGATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
56 3 0.07
57 11 0.24
58 20 0.44
59 2 0.04
60 9 0.20
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (56 bp):
TATTAATTATATATATTTTTAGTAAATTATATTAAGAATAATTATATTAAGAATTT
Found at i:20659911 original size:57 final size:57
Alignment explanation
Indices: 20659795--20659923 Score: 136
Period size: 57 Copynumber: 2.2 Consensus size: 57
20659785 TTTTTATATT
* *
20659795 ATTATATATCATGATTTTAGTAAATTCATATAAGAATAATTATATTAAGAATTTTATTAA
1 ATTATATAT-AT--TTTTAGTAAATTCATATAAGAATAATTATATTAAGAATATGATTAA
* * *
20659855 ATTATATATATTTTTATTAAATT-ATATTTAATAATAATTATGTTAA-AATATGATTAA
1 ATTATATATATTTTTAGTAAATTCATA--TAAGAATAATTATATTAAGAATATGATTAA
* *
20659912 AATATTTATATT
1 ATTATATATATT
20659924 ATATTATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
56 3 0.05
57 30 0.50
58 16 0.27
59 2 0.03
60 9 0.15
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.49
Consensus pattern (57 bp):
ATTATATATATTTTTAGTAAATTCATATAAGAATAATTATATTAAGAATATGATTAA
Found at i:20659918 original size:35 final size:37
Alignment explanation
Indices: 20659878--20659954 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 37
20659868 TTATTAAATT
20659878 ATATTTAATAATA-ATTATGTTAA-AATATGATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
* * * *
20659913 ATATTT-ATATTATATTATTTTAATAATCTTATTAAA
1 ATATTTAATAATATATTATGTTAATAATATGATTAAA
20659949 AT-TTTA
1 ATATTTA
20659955 TAACAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 5 0.14
35 18 0.51
36 12 0.34
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
ATATTTAATAATATATTATGTTAATAATATGATTAAA
Found at i:20660086 original size:39 final size:40
Alignment explanation
Indices: 20660030--20660134 Score: 106
Period size: 44 Copynumber: 2.5 Consensus size: 40
20660020 TTCCCTTATG
* *
20660030 CTATTACACCTCCATTCCATTCAACCAAACACA-AGAA-TA
1 CTATTACGCCTCTATTCCATTCAACCAAACA-ATAGAATTA
* *
20660069 CTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGAATTG
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAATAGAATTA
20660114 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
20660135 ACAGCAAACC
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
39 14 0.25
40 5 0.09
43 1 0.02
44 18 0.33
45 17 0.31
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.31
Consensus pattern (40 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAATAGAATTA
Found at i:20660103 original size:44 final size:45
Alignment explanation
Indices: 20660040--20660137 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
20660030 CTATTACACC
*
20660040 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* *
20660084 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
20660129 TCCATTACA
1 TCCATTACA
20660138 GCAAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.47
45 25 0.51
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.31
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:20670089 original size:46 final size:46
Alignment explanation
Indices: 20670022--20670264 Score: 173
Period size: 46 Copynumber: 5.5 Consensus size: 46
20670012 TCGCATCAGG
20670022 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
* * ** * *
20670068 TCTTATCTCCCTGAGATTACAGCGGAAAAGATTGAAGCCAGT--A-A
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG-AATTACAGA
* * *** ** * *
20670112 TCCTATTTCCCTGAGATTACAGTGGAGCGGA-TTAA-AATAAAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
** * * * * * *
20670156 TCTTATCTCTTTGAAATTACAGTAGAGTAGATC---GCA-T-CAGG
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
* *
20670197 TCTTATCTCCCTGAGGTTACAATGGAATAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
*
20670243 TCTTATCTCCCTAAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
20670265 CGGAGCAGAT
Statistics
Matches: 144, Mismatches: 42, Indels: 22
0.69 0.20 0.11
Matches are distributed among these distances:
41 28 0.19
43 5 0.03
44 52 0.36
45 2 0.01
46 55 0.38
47 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAGA
Found at i:20670232 original size:175 final size:175
Alignment explanation
Indices: 20669892--20670392 Score: 826
Period size: 175 Copynumber: 2.9 Consensus size: 175
20669882 GAAGATGGCG
* *
20669892 GATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATCA
1 GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
* ** *
20669957 TAGTGGAACGGATTAAAA-AAGTGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
*
20670021 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACA
131 GTCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTACA
* **
20670066 GATCTTATCTCCCTGAGATTACAGCGGAAAAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
1 GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
* *
20670131 CAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTTTGAAATTACAGTAGAGTAGATCGCATCAG
66 CAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
*
20670196 GTCTTATCTCCCTGAGGTTACAATGGAATAGACCGAAGAATTACA
131 GTCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTACA
20670241 GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
1 GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
* * *
20670306 CAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCT-AAAGTTACAGTTGAGTAGATCGCATCA
66 CAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTGAAA-TTACAGTAGAGTAGATCGCATCA
*
20670370 GGTCTTATCTCACTGAGATTACA
130 GGTCTTATCTCCCTGAGATTACA
20670393 GCGGAGCAGA
Statistics
Matches: 302, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
174 79 0.26
175 223 0.74
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (175 bp):
GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTA
CAGTGGAACGGATTAAAATAAAAGATCTTATCTCTCTGAAATTACAGTAGAGTAGATCGCATCAG
GTCTTATCTCCCTGAGATTACAATGGAATAGACCGAAGAATTACA
Found at i:20670400 original size:129 final size:127
Alignment explanation
Indices: 20670243--20670520 Score: 441
Period size: 129 Copynumber: 2.2 Consensus size: 127
20670233 GAATTACAGA
* * *
20670243 TCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTACA
*
20670308 GTGGAAC-AGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTTGAGTAGATCGCATCAGG
66 GTGGAACGAG-TTAAAATAAAGGATCTTA--TCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
* *
20670372 TCTTATCTCACTGAGATTACAGCGGAGCAGATTAAAGCTAGTAATCCTATCTCCCTGAGATTACA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTACA
* * *
20670437 GTGGAGCGAGTTAAAATAAAGGATCTTATCTCTGAAGTTACAGTAGAGTAGATCGTATCAGG
66 GTGGAACGAGTTAAAATAAAGGATCTTATCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
20670499 TCTTATCTCCCTGAGATTACAG
1 TCTTATCTCCCTGAGATTACAG
20670521 TGGAATAAAC
Statistics
Matches: 138, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
127 52 0.38
129 84 0.61
130 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (127 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTAAAGCCAGTAATCCTATCTCCCTGAGATTACA
GTGGAACGAGTTAAAATAAAGGATCTTATCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
Found at i:20670467 original size:44 final size:43
Alignment explanation
Indices: 20669891--20670524 Score: 242
Period size: 44 Copynumber: 14.7 Consensus size: 43
20669881 CGAAGATGGC
* * ***
20669891 GGATCTTATCTCCCTAAGATTACAGTGGAGCAGATTGAAGCCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * * * * *
20669934 GTAATCCTATTTCCCTGAGATCATAGTGGAACGGATTAAAA-AA
1 G-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * *** *
20669977 GTGATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCATCA
1 G-GATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAA
** **
20670020 GG-TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-TA-A
* ** * ***
20670066 -GATCTTATCTCCCTGAGATTACAGCGGAAAAGATTGAAGCCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * *
20670108 GTAATCCTATTTCCCTGAGATTACAGTGGAGCGGATTAAAATAAA
1 G-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AA
* ** * * * *** *
20670153 AGATCTTATCTCTTTGAAATTACAGTAGAGTAGA-TCGCATCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * ** **
20670195 GG-TCTTATCTCCCTGAGGTTACAATGGAATAGACCGAAGAATTACA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAA-AA-TA-A
* * * ***
20670241 -GATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCCA
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
* * * *
20670283 GTAATCCTATTTCCCTGAGATTACAGTGGAACAGATTAAAATAAA
1 G-GATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAAT-AA
* * * * *** *
20670328 GGATCTTATCTCTCT-AAAGTTACAGTTGAGTAGA-TCGCATCA
1 GGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAA
* * *
20670370 GG-TCTTATCTCACTGAGATTACAGCGGAGCAGATTAAAGCT-A
1 GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA-ATAA
* *
20670412 GTAATCCTATCTCCCTGAGATTACAGTGGAGC-GAGTTAAAATAAA
1 G-GATCTTATCTCCCTGAGATTACAGTGGAGCAGA-TTAAAAT-AA
* * *** *
20670457 GGATCTTATCT--CTGA-AGTTACAGTAGAGTAGA-TCGTATCA
1 GGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAA
20670497 GG-TCTTATCTCCCTGAGATTACAGTGGA
1 GGATCTTATCTCCCTGAGATTACAGTGGA
20670525 ATAAACTGAA
Statistics
Matches: 419, Mismatches: 136, Indels: 74
0.67 0.22 0.12
Matches are distributed among these distances:
39 8 0.02
40 3 0.01
41 90 0.21
42 32 0.08
43 41 0.10
44 178 0.42
45 11 0.03
46 56 0.13
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
GGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAA
Found at i:20670985 original size:11 final size:11
Alignment explanation
Indices: 20670967--20670996 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20670957 AGTAAAACCC
20670967 AAATATAAAAT
1 AAATATAAAAT
*
20670978 ATATATAAAAT
1 AAATATAAAAT
20670989 AAATATAA
1 AAATATAA
20670997 TAAAAGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATATAAAAT
Found at i:20679409 original size:15 final size:16
Alignment explanation
Indices: 20679375--20679408 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
20679365 TAACCACTTT
20679375 AAAATAAAATCAAATA
1 AAAATAAAATCAAATA
20679391 AAAAT-AAAT-AAATA
1 AAAATAAAATCAAATA
20679405 AAAA
1 AAAA
20679409 AGATTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 4 0.22
16 5 0.28
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAAATCAAATA
Found at i:20680509 original size:21 final size:20
Alignment explanation
Indices: 20680477--20680516 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
20680467 GTTTTCAAAT
20680477 ATAATATTGTTTTA-AATAG
1 ATAATATTGTTTTACAATAG
20680496 ATAATTATGTGTTTTACAATA
1 ATAA-TAT-TGTTTTACAATA
20680517 TTTTAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 3 0.17
21 7 0.39
22 4 0.22
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATAATATTGTTTTACAATAG
Found at i:20688815 original size:25 final size:25
Alignment explanation
Indices: 20688767--20688815 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
20688757 AATAATTGAA
* * *
20688767 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
20688792 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
20688816 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:20689169 original size:18 final size:18
Alignment explanation
Indices: 20689146--20689186 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20689136 TGGTTGGATT
*
20689146 CGTGTAT-TCGTCTGAGTC
1 CGTGTATCT-GTCCGAGTC
20689164 CGTGTATCTGTCCGAGTC
1 CGTGTATCTGTCCGAGTC
20689182 CGTGT
1 CGTGT
20689187 CGTGTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.10, C:0.24, G:0.29, T:0.37
Consensus pattern (18 bp):
CGTGTATCTGTCCGAGTC
Found at i:20690195 original size:13 final size:13
Alignment explanation
Indices: 20690179--20690207 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20690169 GTCGCACACC
20690179 GGCAACACACATG
1 GGCAACACACATG
20690192 GGCAACACACATG
1 GGCAACACACATG
20690205 GGC
1 GGC
20690208 GTGTGACCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.31, G:0.28, T:0.07
Consensus pattern (13 bp):
GGCAACACACATG
Found at i:20693301 original size:25 final size:25
Alignment explanation
Indices: 20693263--20693341 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
20693253 AGCACTCTCT
*
20693263 TGAGCCATAAAACAAGATGCTCATG
1 TGAGCCATAAAACAAGAAGCTCATG
** * *
20693288 TGAGCCATGTAACAGGAAGCTCATA
1 TGAGCCATAAAACAAGAAGCTCATG
* ** *
20693313 AGAG-TTTAAAACAGGAAGCTCAT-
1 TGAGCCATAAAACAAGAAGCTCATG
20693336 TGAGCC
1 TGAGCC
20693342 TAATAGGTAA
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
23 3 0.07
24 15 0.37
25 23 0.56
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (25 bp):
TGAGCCATAAAACAAGAAGCTCATG
Found at i:20698145 original size:19 final size:18
Alignment explanation
Indices: 20698109--20698154 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
20698099 AATATTTAGT
* *
20698109 TTAAGTATTAAATGTGTC
1 TTAAGTATTTAATATGTC
20698127 TTAAGTTATTTAATATGTC
1 TTAAG-TATTTAATATGTC
20698146 -TAAGTATTT
1 TTAAGTATTT
20698155 TTGGCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAAGTATTTAATATGTC
Found at i:20703593 original size:15 final size:15
Alignment explanation
Indices: 20703565--20703601 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
20703555 CGAGAAGAGA
20703565 AAAATG-AA-AAAAG
1 AAAATGAAATAAAAG
*
20703578 AAATTGAAATAAAAG
1 AAAATGAAATAAAAG
20703593 AAAATGAAA
1 AAAATGAAA
20703602 AAGAAAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 5 0.25
14 2 0.10
15 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
AAAATGAAATAAAAG
Found at i:20703689 original size:33 final size:33
Alignment explanation
Indices: 20703648--20703776 Score: 127
Period size: 33 Copynumber: 3.9 Consensus size: 33
20703638 AATGTGAATG
*
20703648 AAACGAGTGCAAAAGAAAGAGAGCTCAAAAAGA
1 AAACGAGTGAAAAAGAAAGAGAGCTCAAAAAGA
* * **
20703681 AAATGAGTGAAAAAGAAAGAGTGCTTGAAAAGA
1 AAACGAGTGAAAAAGAAAGAGAGCTCAAAAAGA
* *
20703714 AAACAAGTGAAAAAGAGAA-AGAGCTTGAAAAAG-
1 AAACGAGTGAAAAAGA-AAGAGAGC-TCAAAAAGA
* * *
20703747 AAACGTGTGAAGAAGAAGAGAGTGCTCAAA
1 AAACGAGTGAAAAAGAA-AGAGAGCTCAAA
20703777 CACAAGGGAG
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
32 1 0.01
33 64 0.83
34 12 0.16
ACGTcount: A:0.55, C:0.08, G:0.26, T:0.11
Consensus pattern (33 bp):
AAACGAGTGAAAAAGAAAGAGAGCTCAAAAAGA
Found at i:20703693 original size:16 final size:15
Alignment explanation
Indices: 20703647--20703770 Score: 70
Period size: 17 Copynumber: 7.7 Consensus size: 15
20703637 AAATGTGAAT
* *
20703647 GAAACGAGTGCAAAA
1 GAAAAGAGTGAAAAA
*
20703662 GAAAGAGAGCTCAAAAA
1 GAAA-AGAG-TGAAAAA
20703679 GAAAATGAGTGAAAAA
1 GAAAA-GAGTGAAAAA
*
20703695 G-AAAGAGTGCTTGAAAA
1 GAAAAGAGTG---AAAAA
*
20703712 GAAAACAAGTGAAAAA
1 GAAAA-GAGTGAAAAA
20703728 GAGAAAGAGCTTGAAAAA
1 GA-AAAGAG--TGAAAAA
* * *
20703746 GAAACGTGTGAAGAA
1 GAAAAGAGTGAAAAA
*
20703761 GAAGAGAGTG
1 GAAAAGAGTG
20703771 CTCAAACACA
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
14 5 0.06
15 20 0.24
16 19 0.23
17 24 0.29
18 12 0.14
19 4 0.05
ACGTcount: A:0.55, C:0.06, G:0.28, T:0.10
Consensus pattern (15 bp):
GAAAAGAGTGAAAAA
Found at i:20703757 original size:66 final size:67
Alignment explanation
Indices: 20703648--20703772 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 67
20703638 AATGTGAATG
* * *
20703648 AAACGAGTGCAAAAGAAAGAGAGCTCAAAAAGAAAATGAGTGAAAAAGAA-AGAGTGCTTGAAAA
1 AAACAAGTGAAAAAGAAAGAGAGCTCAAAAAGAAAACGAGTGAAAAAGAAGAGAGTGCTTGAAAA
20703712 GA
66 GA
* * *
20703714 AAACAAGTGAAAAAGAGAA-AGAGCTTGAAAAAG-AAACGTGTGAAGAAGAAGAGAGTGCT
1 AAACAAGTGAAAAAGA-AAGAGAGC-TCAAAAAGAAAACGAGTGAAAAAGAAGAGAGTGCT
20703773 CAAACACAAG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
66 33 0.66
67 17 0.34
ACGTcount: A:0.54, C:0.07, G:0.27, T:0.11
Consensus pattern (67 bp):
AAACAAGTGAAAAAGAAAGAGAGCTCAAAAAGAAAACGAGTGAAAAAGAAGAGAGTGCTTGAAAA
GA
Found at i:20706107 original size:19 final size:18
Alignment explanation
Indices: 20706071--20706116 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
20706061 AATATTTAGT
* *
20706071 TTAAGTATTAAATGTGTC
1 TTAAGTATTTAATATGTC
20706089 TTAAGTTATTTAATATGTC
1 TTAAG-TATTTAATATGTC
20706108 -TAAGTATTT
1 TTAAGTATTT
20706117 TCGGCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 5 0.20
18 9 0.36
19 11 0.44
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (18 bp):
TTAAGTATTTAATATGTC
Found at i:20711586 original size:18 final size:19
Alignment explanation
Indices: 20711550--20711586 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
20711540 ATTTGATTCC
*
20711550 TTTTGAATCAACTCGAATA
1 TTTTGAATCAACTCAAATA
20711569 TTTTGAAT-AACTCAAATA
1 TTTTGAATCAACTCAAATA
20711587 ATAAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTTGAATCAACTCAAATA
Found at i:20713252 original size:19 final size:20
Alignment explanation
Indices: 20713218--20713284 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 20
20713208 ATTATAAAAA
20713218 TATACAAAATTA-TAATTTTT
1 TATA-AAAATTATTAATTTTT
*
20713238 TATAAAAA-TATTAA-TATT
1 TATAAAAATTATTAATTTTT
*
20713256 TATAAGAAATTATAAATATTTT
1 TATAA-AAATTATTAAT-TTTT
*
20713278 TTTAAAA
1 TATAAAA
20713285 TTTTAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
18 10 0.26
19 10 0.26
20 9 0.24
21 2 0.05
22 7 0.18
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (20 bp):
TATAAAAATTATTAATTTTT
Found at i:20713275 original size:20 final size:19
Alignment explanation
Indices: 20713218--20713276 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
20713208 ATTATAAAAA
* *
20713218 TATACAAAATTATAATTTTT
1 TATA-AAAATTATAAATATT
*
20713238 TATAAAAA-TATTAATATT
1 TATAAAAATTATAAATATT
20713256 TATAAGAAATTATAAATATT
1 TATAA-AAATTATAAATATT
20713276 T
1 T
20713277 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 12 0.36
19 7 0.21
20 14 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
TATAAAAATTATAAATATT
Found at i:20713285 original size:20 final size:20
Alignment explanation
Indices: 20713223--20713291 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
20713213 AAAAATATAC
*
20713223 AAAATTAT-AAT-TTTTTAT
1 AAAATTATAAATATTTTTTT
* * * *
20713241 AAAAATATTAATA-TTTATA
1 AAAATTATAAATATTTTTTT
20713260 AGAAATTATAAATATTTTTTT
1 A-AAATTATAAATATTTTTTT
*
20713281 AAAATTTTAAA
1 AAAATTATAAA
20713292 GAATTAATAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
18 7 0.18
19 7 0.18
20 19 0.50
21 5 0.13
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (20 bp):
AAAATTATAAATATTTTTTT
Found at i:20713464 original size:19 final size:19
Alignment explanation
Indices: 20713440--20713492 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
20713430 TAAATTCGTA
*
20713440 AATAATTTTTATAATATTT
1 AATAATTTTTATAATAATT
* *
20713459 ACTAATTTTTACAA-AATT
1 AATAATTTTTATAATAATT
20713477 AATAATTATTTATAAT
1 AATAATT-TTTATAAT
20713493 TCTCAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 9 0.33
19 18 0.67
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AATAATTTTTATAATAATT
Found at i:20713998 original size:26 final size:27
Alignment explanation
Indices: 20713968--20714026 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
20713958 AAAAGCCGTT
*
20713968 TTTTTTTA-ATTTACCGAAATGGACCGA
1 TTTTTTGATATTTACCGAAATGGACC-A
* *
20713995 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTGA-TATTTACCGAAATGGACCA
20714023 TTTT
1 TTTT
20714027 CCGGGAAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.26
28 5 0.19
29 15 0.56
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTTTTGATATTTACCGAAATGGACCA
Found at i:20726218 original size:19 final size:19
Alignment explanation
Indices: 20726185--20726230 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
20726175 AACAGAAAAT
* *
20726185 AAATCAAATATAAAACCAAA
1 AAAT-AAATAAAAAAACAAA
*
20726205 AAATAAATAAAAAAACAAC
1 AAATAAATAAAAAAACAAA
20726224 AAATAAA
1 AAATAAA
20726231 GTCCATTGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (19 bp):
AAATAAATAAAAAAACAAA
Found at i:20730734 original size:30 final size:30
Alignment explanation
Indices: 20730699--20730767 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
20730689 GAAAGAGATT
20730699 TCTCTTCTTTTGGGGTGAAAACAAAAATTC
1 TCTCTTCTTTTGGGGTGAAAACAAAAATTC
*
20730729 TCTCTTCTTTTGGGTTGAAAACAAAAATTC
1 TCTCTTCTTTTGGGGTGAAAACAAAAATTC
20730759 TCTCTTCTT
1 TCTCTTCTT
20730768 AATAGAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (30 bp):
TCTCTTCTTTTGGGGTGAAAACAAAAATTC
Found at i:20733735 original size:23 final size:23
Alignment explanation
Indices: 20733708--20733754 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
20733698 TGGTAGATCC
20733708 ATTGGATATAGTTGGCATGCCAT
1 ATTGGATATAGTTGGCATGCCAT
20733731 ATTGGATATAGTTGGCATGCCAT
1 ATTGGATATAGTTGGCATGCCAT
20733754 A
1 A
20733755 GGATTTGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.34
Consensus pattern (23 bp):
ATTGGATATAGTTGGCATGCCAT
Found at i:20737419 original size:16 final size:16
Alignment explanation
Indices: 20737406--20737440 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20737396 AAAGATTGAG
20737406 ATTTCTAAATATTGCA
1 ATTTCTAAATATTGCA
*
20737422 ATTTCTAAATATTGGA
1 ATTTCTAAATATTGCA
20737438 ATT
1 ATT
20737441 CCATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (16 bp):
ATTTCTAAATATTGCA
Found at i:20738381 original size:17 final size:17
Alignment explanation
Indices: 20738359--20738392 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
20738349 CCTTAGAATT
20738359 TATGTGAAGTAACAGGG
1 TATGTGAAGTAACAGGG
20738376 TATGTGAAGTAACAGGG
1 TATGTGAAGTAACAGGG
20738393 ATGAATTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (17 bp):
TATGTGAAGTAACAGGG
Found at i:20739913 original size:51 final size:51
Alignment explanation
Indices: 20739741--20740033 Score: 295
Period size: 51 Copynumber: 5.8 Consensus size: 51
20739731 CTTTTATCAT
* * **
20739741 TCGATACACATAGTAGCCTTCACATGGTACTACACACGTGATCAAGTTTTA
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * * **
20739792 -CGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * *
20739842 -CGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
* * * * *
20739892 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAA-AGCTTC
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACA-TTTA
* * * * * * *
20739943 TTGGTACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTA
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
** *
20739994 TCGATACATGTAGTAGCCTTCACACAGTACTACACACGTG
1 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTG
20740034 TTCATCGATA
Statistics
Matches: 199, Mismatches: 40, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
50 89 0.45
51 109 0.55
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (51 bp):
TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGACCAACATTTA
Found at i:20739984 original size:102 final size:100
Alignment explanation
Indices: 20739745--20740033 Score: 402
Period size: 102 Copynumber: 2.9 Consensus size: 100
20739735 TATCATTCGA
* * * * *** *
20739745 TACACATAGTAGCCTTCACATGGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* *
20739809 TTCACATAGTACTACACACGTGATCAAGTTTTACGG
66 TTCACACAGTACTACACACGTGACCAAGTTTTA-GG
20739845 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
20739910 TTCACACAGTACTACACACGTGACCAAAGCTTCTT-GG
66 TTCACACAGTACTACACACGTGACC-AAG-TT-TTAGG
* * * *
20739947 TACATATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATACATGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
20740012 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
20740034 TTCATCGATA
Statistics
Matches: 171, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
100 40 0.23
101 39 0.23
102 88 0.51
103 2 0.01
104 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (100 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAGTTTTAGG
Found at i:20757824 original size:94 final size:94
Alignment explanation
Indices: 20757663--20757842 Score: 360
Period size: 94 Copynumber: 1.9 Consensus size: 94
20757653 TTATACTTGA
20757663 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
1 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
20757728 ACCATGAATTTTGGAAAGGAGAGGTTGTT
66 ACCATGAATTTTGGAAAGGAGAGGTTGTT
20757757 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
1 GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
20757822 ACCATGAATTTTGGAAAGGAG
66 ACCATGAATTTTGGAAAGGAG
20757843 CTAGATGGTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.39
Consensus pattern (94 bp):
GGTATGGCTAATAGGTTTACTAAAAATAGTTTGAAATTCCCTTAGGTTTTTCTTACTCTTGGTTG
ACCATGAATTTTGGAAAGGAGAGGTTGTT
Found at i:20760004 original size:110 final size:110
Alignment explanation
Indices: 20759811--20760141 Score: 617
Period size: 110 Copynumber: 3.0 Consensus size: 110
20759801 ATGTCTCTAC
*
20759811 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACGACAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACAACAT
*
20759876 AATAATCCTTCTTAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
20759921 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACAACAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACAACAT
*
20759986 AATAATCTTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
* *
20760031 TCATGGAGTCAACTACTCTTATAGCTAAGACTAGTGATCTCCTCAATTGGAATTGTAGACAACAT
1 TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACAACAT
20760096 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
66 AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
20760141 T
1 T
20760142 TATGAGATTA
Statistics
Matches: 215, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 215 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.35
Consensus pattern (110 bp):
TCATGGAGTCAACTACTCTTATAGCCAAGACTAGCGATCTCCTCAATTGGAATTGTAGACAACAT
AATAATCCTTCTCAGTATTTGAATCAAATGCTCACTTTGATTCTT
Found at i:20770173 original size:26 final size:26
Alignment explanation
Indices: 20770136--20770193 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
20770126 CCCAACAAAT
*
20770136 TTTTGACAATTTTACCCTTGGTAAAA
1 TTTTGACAATTTTACCCCTGGTAAAA
* *
20770162 TTTTGACGATTTTTCCCCTGGTAAAA
1 TTTTGACAATTTTACCCCTGGTAAAA
20770188 TTTTGA
1 TTTTGA
20770194 GAAGATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (26 bp):
TTTTGACAATTTTACCCCTGGTAAAA
Found at i:20772267 original size:10 final size:10
Alignment explanation
Indices: 20772204--20772290 Score: 68
Period size: 10 Copynumber: 8.4 Consensus size: 10
20772194 TTCTGCCCAA
20772204 TTATAA-TTT
1 TTATAATTTT
20772213 TTATAATTTTTT
1 TTATAA--TTTT
* *
20772225 TCTACAATTTG
1 T-TATAATTTT
*
20772236 TTATAAGTTT
1 TTATAATTTT
* *
20772246 ATATAATATT
1 TTATAATTTT
*
20772256 TTACAATTTT
1 TTATAATTTT
20772266 TTAATAATTTT
1 TT-ATAATTTT
*
20772277 TAATAATTTT
1 TTATAATTTT
20772287 TTAT
1 TTAT
20772291 TTACATCCGG
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
9 6 0.10
10 33 0.56
11 12 0.20
12 4 0.07
13 4 0.07
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (10 bp):
TTATAATTTT
Found at i:20772284 original size:21 final size:22
Alignment explanation
Indices: 20772243--20772290 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
20772233 TTGTTATAAG
20772243 TTTATATAATATTTTACAATTT
1 TTTATATAATATTTTACAATTT
*
20772265 TTTA-ATAAT-TTTTAATAATTT
1 TTTATATAATATTTT-ACAATTT
20772286 TTTAT
1 TTTAT
20772291 TTACATCCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATATAATATTTTACAATTT
Found at i:20772289 original size:31 final size:30
Alignment explanation
Indices: 20772204--20772289 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
20772194 TTCTGCCCAA
20772204 TTATAATTTTT-ATAATTTTTTTCTACAATTTG
1 TTATAATTTTTAATAA--TTTTT-TACAATTTG
* * *
20772236 TTATAA-GTTTATATAATATTTTACAATTTT
1 TTATAATTTTTA-ATAATTTTTTACAATTTG
20772266 TTAATAATTTTTAATAATTTTTTA
1 TT-ATAATTTTTAATAATTTTTTA
20772290 TTTACATCCG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 10 0.22
31 21 0.47
32 10 0.22
33 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (30 bp):
TTATAATTTTTAATAATTTTTTACAATTTG
Found at i:20773383 original size:18 final size:18
Alignment explanation
Indices: 20773346--20773381 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
20773336 CTTCAATATG
*
20773346 TAATTAAATTTTATTATT
1 TAATTAAATTTCATTATT
20773364 TAATT-AATTTCATTATT
1 TAATTAAATTTCATTATT
20773381 T
1 T
20773382 TATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTAAATTTCATTATT
Found at i:20773788 original size:33 final size:32
Alignment explanation
Indices: 20773730--20773798 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 32
20773720 TCCAGAATCG
* * *
20773730 TGAATCTAAACCCGAACCTTGAACCCTAACTT
1 TGAATCTAAACCCGAACCTTAAACCCAAACCT
20773762 TGAATGCTAAACCCTGAACC-TAAACCCAAACCT
1 TGAAT-CTAAACCC-GAACCTTAAACCCAAACCT
20773795 TGAA
1 TGAA
20773799 CATTGGATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.16
33 22 0.69
34 5 0.16
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.22
Consensus pattern (32 bp):
TGAATCTAAACCCGAACCTTAAACCCAAACCT
Found at i:20774890 original size:17 final size:17
Alignment explanation
Indices: 20774868--20774904 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
20774858 AGGGGATAAG
20774868 AACCCGTACAACCACAT
1 AACCCGTACAACCACAT
20774885 AACCCGTACAACCACAT
1 AACCCGTACAACCACAT
20774902 AAC
1 AAC
20774905 ATGTAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.41, G:0.05, T:0.11
Consensus pattern (17 bp):
AACCCGTACAACCACAT
Found at i:20777675 original size:13 final size:14
Alignment explanation
Indices: 20777650--20777677 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20777640 AAAACTTATT
20777650 AAAAATTCAAAAAA
1 AAAAATTCAAAAAA
20777664 AAAAATTCAAAAAA
1 AAAAATTCAAAAAA
20777678 TTCATGGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAATTCAAAAAA
Found at i:20779873 original size:43 final size:43
Alignment explanation
Indices: 20779821--20779902 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
20779811 CGCTTTAGTG
**
20779821 GAAGCGCCGCTAAAGACCTTGATCTGTAGCGGCGTTTTTGGTA
1 GAAGCGCCGCTAAAGACCAGGATCTGTAGCGGCGTTTTTGGTA
* * *
20779864 GAAGCGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTT
1 GAAGCGCCGCTAAAGACCAGGATCTGTAGCGGCGTTTTT
20779903 ATCCCAAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (43 bp):
GAAGCGCCGCTAAAGACCAGGATCTGTAGCGGCGTTTTTGGTA
Found at i:20779977 original size:43 final size:42
Alignment explanation
Indices: 20779930--20780134 Score: 193
Period size: 43 Copynumber: 4.8 Consensus size: 42
20779920 AGAGTAAGAC
* *
20779930 CTTTAGCGGCGCTTCT-CCCAAAAACGCCGCTAAAGAACCTATT
1 CTTTAGCGGCGCTT-TGACCAAAAACGCCACTAAAG-ACCTATT
* * *
20779973 CTTTAGCGGTGCTTTGACCATAAACGCCCCTAAAGACCTATT
1 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCTATT
* ** * *
20780015 CTTTAGTGGCGCTTTCCCCTAAAACGCCGC-AATAGACTCTGA-T
1 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAA-AGAC-CT-ATT
* ** *
20780058 CTGTAGCGGCGCTTTTTCCACAAACGCCACTAAAGACCCT-TAT
1 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGA-CCTAT-T
20780101 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
1 CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAA
20780135 ACGGCCACCA
Statistics
Matches: 132, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 35 0.27
43 91 0.69
44 4 0.03
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCTATT
Found at i:20780065 original size:85 final size:87
Alignment explanation
Indices: 20779930--20780134 Score: 219
Period size: 85 Copynumber: 2.4 Consensus size: 87
20779920 AGAGTAAGAC
* * *
20779930 CTTTAGCGGCGC-TTCTCCCAAAAACGCCGCTAAAGAACCTATTCTTTAGCGGTGCTTTGACCAT
1 CTTTAGCGGCGCTTTCTCCCAAAAACGCCGCTAAAGAACCTATTCTGTAGCGGCGCTTTGACCAC
*
20779994 AAACGCCCCTAAAGA-CC-TATT
66 AAACGCCACTAAAGACCCTTA-T
* * **
20780015 CTTTAGTGGCGCTTTC-CCCTAAAACGCCGC-AATAG-ACTCTGA-TCTGTAGCGGCGCTTTTTC
1 CTTTAGCGGCGCTTTCTCCCAAAAACGCCGCTAA-AGAAC-CT-ATTCTGTAGCGGCGCTTTGAC
20780076 CACAAACGCCACTAAAGACCCTTAT
63 CACAAACGCCACTAAAGACCCTTAT
** *
20780101 CTTTAGCGGCGCTTT-GACCAAAAACGCCACTAAA
1 CTTTAGCGGCGCTTTCTCCCAAAAACGCCGCTAAA
20780135 ACGGCCACCA
Statistics
Matches: 100, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
84 4 0.04
85 59 0.59
86 33 0.33
87 4 0.04
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (87 bp):
CTTTAGCGGCGCTTTCTCCCAAAAACGCCGCTAAAGAACCTATTCTGTAGCGGCGCTTTGACCAC
AAACGCCACTAAAGACCCTTAT
Found at i:20780532 original size:21 final size:21
Alignment explanation
Indices: 20780490--20780581 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
20780480 TTTGACGCTG
**
20780490 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
20780511 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
20780532 CTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
20780553 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
20780574 ATCTGCTT
1 CTCTGCTT
20780582 TAAGCTGCTG
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:20780629 original size:66 final size:66
Alignment explanation
Indices: 20780552--20780698 Score: 199
Period size: 66 Copynumber: 2.2 Consensus size: 66
20780542 CTCGCTGCCG
* * *
20780552 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCACATCTGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
20780615 GAA
64 GAA
* * * *
20780618 CCTCAGCTTCTCTCGCTGCTACATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCACATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
20780683 A
66 A
20780684 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
20780699 ATGTTGCCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCACATCTGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:20780714 original size:66 final size:66
Alignment explanation
Indices: 20780573--20780721 Score: 185
Period size: 66 Copynumber: 2.3 Consensus size: 66
20780563 CTTGCTGCCG
* * *
20780573 CATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGC
1 CATCCGCTTTAAGTTG-TAGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGC
20780637 TA
65 TA
* * * *
20780639 CATCTGCTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGT
1 CATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGC
*
20780703 TG
65 TA
*
20780705 CCTCCGCTTTAAGTTGT
1 CATCCGCTTTAAGTTGT
20780722 GTAATTTGCT
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (66 bp):
CATCCGCTTTAAGTTGTAGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGCT
A
Found at i:20786169 original size:16 final size:16
Alignment explanation
Indices: 20786148--20786201 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
20786138 ATTAAGCTAC
20786148 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
20786164 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
* *
20786180 GAAAATTATGTAAGTTAT
1 GTAAGTTATGT-A-TTAT
20786198 GTAA
1 GTAA
20786202 TTTACGAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 23 0.74
17 1 0.03
18 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:20786197 original size:9 final size:9
Alignment explanation
Indices: 20786148--20786266 Score: 71
Period size: 9 Copynumber: 14.3 Consensus size: 9
20786138 ATTAAGCTAC
20786148 GTAAGTTAT
1 GTAAGTTAT
20786157 GT-A-TTAT
1 GTAAGTTAT
20786164 GTAAGTTAT
1 GTAAGTTAT
*
20786173 -TTA-TTAT
1 GTAAGTTAT
* *
20786180 GAAAATTAT
1 GTAAGTTAT
20786189 GTAAGTTAT
1 GTAAGTTAT
* *
20786198 GTAATTTAC
1 GTAAGTTAT
*
20786207 G-AA-TAAT
1 GTAAGTTAT
** *
20786214 -TAAAAATAA
1 GT-AAGTTAT
20786223 GTAAGTTAT
1 GTAAGTTAT
20786232 GTAAG-T-T
1 GTAAGTTAT
20786239 GTAAGTTAT
1 GTAAGTTAT
20786248 GTAAG-T-T
1 GTAAGTTAT
20786255 GTAAGTTAT
1 GTAAGTTAT
20786264 GTA
1 GTA
20786267 TAATATTAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
7 24 0.29
8 13 0.16
9 45 0.54
10 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.43
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:20786200 original size:34 final size:34
Alignment explanation
Indices: 20786153--20786238 Score: 86
Period size: 34 Copynumber: 2.6 Consensus size: 34
20786143 GCTACGTAAG
*** *
20786153 TTATGT-A-TTATGTAAGTTATTTATTATGAAAA
1 TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
* *
20786185 TTATGTAAGTTATGTAATTTACGAATAATTAAAA
1 TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
* *
20786219 ATAAGTAAGTTATGTAAGTT
1 TTATGTAAGTTATGTAAGTT
20786239 GTAAGTTATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
32 6 0.14
33 1 0.02
34 36 0.84
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAGTTACGAATAATGAAAA
Done.